Penghusuchus pani gen. et sp. nov. is described on the basis of a skeleton from the upper Miocene of Penghu Island. It is the most complete vertebrate fossil from Taiwan. Penghusuchus pani is distinguished from other tomistomines mainly in features of the skull and mandible. The most diagnostic characters for the taxon are that the prefrontal and anterior process of the jugal extend as anteriorly as the lacrimal does; the seventh maxillary tooth is the largest; the choana is sharply triangular in outline; and the floor of the nasopharyngeal canal and choanal borders strongly drop downward to form a Y-shaped prominence on the ventral surface of the pterygoids. Our phylogenetic analysis indicates that the new form is closely related to two other Asian fossil tomistomines, Tomistoma petrolica from southeastern China and Toyotamaphimeia machikanensis from Japan. The discovery of P. pani certainly enriches our knowledge of the paleogeography and the phylogenetic relationships amongst tomistomines.